# Benchmarking Self-Supervised Learning on Diverse Pathology Datasets

arXiv: https://arxiv.org/abs/2212.04690 · HTML: https://mlsanity.com/paper/2212.04690/

## Key facts

- Cited by 150 papers in the map (data through 14 Oct 2026).
- Builds on 46 of its 72 references that are in the map.
- First posted on arXiv 9 Dec 2022.

## Builds on (most cited first, 30 of 46)

- [Deep Residual Learning for Image Recognition](https://mlsanity.com/paper/1512.03385/) (2015)
- [An Image is Worth 16x16 Words: Transformers for Image Recognition at Scale](https://mlsanity.com/paper/2010.11929/) (2020)
- [A Simple Framework for Contrastive Learning of Visual Representations](https://mlsanity.com/paper/2002.05709/) (2020)
- [Representation Learning with Contrastive Predictive Coding](https://mlsanity.com/paper/1807.03748/) (2018)
- [Momentum Contrast for Unsupervised Visual Representation Learning](https://mlsanity.com/paper/1911.05722/) (2019)
- [Emerging Properties in Self-Supervised Vision Transformers](https://mlsanity.com/paper/2104.14294/) (2021)
- [Bootstrap your own latent: A new approach to self-supervised Learning](https://mlsanity.com/paper/2006.07733/) (2020)
- [Encoder-Decoder with Atrous Separable Convolution for Semantic Image Segmentation](https://mlsanity.com/paper/1802.02611/) (2018)
- [Exploring Simple Siamese Representation Learning](https://mlsanity.com/paper/2011.10566/) (2020)
- [Unsupervised Learning of Visual Features by Contrasting Cluster Assignments](https://mlsanity.com/paper/2006.09882/) (2020)
- [Improved Baselines with Momentum Contrastive Learning](https://mlsanity.com/paper/2003.04297/) (2020)
- [Identity Mappings in Deep Residual Networks](https://mlsanity.com/paper/1603.05027/) (2016)
- [Barlow Twins: Self-Supervised Learning via Redundancy Reduction](https://mlsanity.com/paper/2103.03230/) (2021)
- [Decoupled Weight Decay Regularization](https://mlsanity.com/paper/1711.05101/) (2017)
- [An Empirical Study of Training Self-Supervised Vision Transformers](https://mlsanity.com/paper/2104.02057/) (2021)
- [Accurate, Large Minibatch SGD: Training ImageNet in 1 Hour](https://mlsanity.com/paper/1706.02677/) (2017)
- [Big Self-Supervised Models are Strong Semi-Supervised Learners](https://mlsanity.com/paper/2006.10029/) (2020)
- [Self-Supervised Learning of Pretext-Invariant Representations](https://mlsanity.com/paper/1912.01991/) (2019)
- [Panoptic Segmentation](https://mlsanity.com/paper/1801.00868/) (2018)
- [Data Efficient and Weakly Supervised Computational Pathology on Whole Slide Images](https://mlsanity.com/paper/2004.09666/) (2020)
- [Do Better ImageNet Models Transfer Better?](https://mlsanity.com/paper/1805.08974/) (2018)
- [Large Batch Training of Convolutional Networks](https://mlsanity.com/paper/1708.03888/) (2017)
- [Dual-stream Multiple Instance Learning Network for Whole Slide Image Classification with Self-supervised Contrastive Learning](https://mlsanity.com/paper/2011.08939/) (2020)
- [Rotation Equivariant CNNs for Digital Pathology](https://mlsanity.com/paper/1806.03962/) (2018)
- [HoVer-Net: Simultaneous Segmentation and Classification of Nuclei in Multi-Tissue Histology Images](https://mlsanity.com/paper/1812.06499/) (2018)
- [Rethinking ImageNet Pre-training](https://mlsanity.com/paper/1811.08883/) (2018)
- [Transfusion: Understanding Transfer Learning for Medical Imaging](https://mlsanity.com/paper/1902.07208/) (2019)
- [Scaling Vision Transformers to Gigapixel Images via Hierarchical Self-Supervised Learning](https://mlsanity.com/paper/2206.02647/) (2022)
- [XCiT: Cross-Covariance Image Transformers](https://mlsanity.com/paper/2106.09681/) (2021)
- [Big Self-Supervised Models Advance Medical Image Classification](https://mlsanity.com/paper/2101.05224/) (2021)

## Built on by (most cited first, 30 of 150)

- [Virchow2: Scaling Self-Supervised Mixed Magnification Models in Pathology](https://mlsanity.com/paper/2408.00738/) (2024)
- [HEST-1k: A Dataset for Spatial Transcriptomics and Histology Image Analysis](https://mlsanity.com/paper/2406.16192/) (2024)
- [Virchow: A Million-Slide Digital Pathology Foundation Model](https://mlsanity.com/paper/2309.07778/) (2023)
- [PRISM: A Multi-Modal Generative Foundation Model for Slide-Level Histopathology](https://mlsanity.com/paper/2405.10254/) (2024)
- [Phikon-v2, A large and public feature extractor for biomarker prediction](https://mlsanity.com/paper/2409.09173/) (2024)
- [Morphological Prototyping for Unsupervised Slide Representation Learning in Computational Pathology](https://mlsanity.com/paper/2405.11643/) (2024)
- [Dynamic Graph Representation with Knowledge-aware Attention for Histopathology Whole Slide Image Analysis](https://mlsanity.com/paper/2403.07719/) (2024)
- [A Clinical Benchmark of Public Self-Supervised Pathology Foundation Models](https://mlsanity.com/paper/2407.06508/) (2024)
- [Attention-Challenging Multiple Instance Learning for Whole Slide Image Classification](https://mlsanity.com/paper/2311.07125/) (2023)
- [Hibou: A Family of Foundational Vision Transformers for Pathology](https://mlsanity.com/paper/2406.05074/) (2024)
- [Transcriptomics-guided Slide Representation Learning in Computational Pathology](https://mlsanity.com/paper/2405.11618/) (2024)
- [A General-Purpose Self-Supervised Model for Computational Pathology](https://mlsanity.com/paper/2308.15474/) (2023)
- [RudolfV: A Foundation Model by Pathologists for Pathologists](https://mlsanity.com/paper/2401.04079/) (2024)
- [In-context learning enables multimodal large language models to classify cancer pathology images](https://mlsanity.com/paper/2403.07407/) (2024)
- [Continual Self-supervised Learning: Towards Universal Multi-modal Medical Data Representation Learning](https://mlsanity.com/paper/2311.17597/) (2023)
- [CPath-Omni: A Unified Multimodal Foundation Model for Patch and Whole Slide Image Analysis in Computational Pathology](https://mlsanity.com/paper/2412.12077/) (2024)
- [Computational Pathology at Health System Scale -- Self-Supervised Foundation Models from Three Billion Images](https://mlsanity.com/paper/2310.07033/) (2023)
- [WsiCaption: Multiple Instance Generation of Pathology Reports for Gigapixel Whole-Slide Images](https://mlsanity.com/paper/2311.16480/) (2023)
- [Domain Generalization in Computational Pathology: Survey and Guidelines](https://mlsanity.com/paper/2310.19656/) (2023)
- [Multistain Pretraining for Slide Representation Learning in Pathology](https://mlsanity.com/paper/2408.02859/) (2024)
- [Data-Centric Foundation Models in Computational Healthcare: A Survey](https://mlsanity.com/paper/2401.02458/) (2024)
- [Towards Large-Scale Training of Pathology Foundation Models](https://mlsanity.com/paper/2404.15217/) (2024)
- [A Foundational Multimodal Vision Language AI Assistant for Human Pathology](https://mlsanity.com/paper/2312.07814/) (2023)
- [Knowledge-enhanced Pretraining for Vision-language Pathology Foundation Model on Cancer Diagnosis](https://mlsanity.com/paper/2412.13126/) (2024)
- [CPLIP: Zero-Shot Learning for Histopathology with Comprehensive Vision-Language Alignment](https://mlsanity.com/paper/2406.05205/) (2024)
- [Vim4Path: Self-Supervised Vision Mamba for Histopathology Images](https://mlsanity.com/paper/2404.13222/) (2024)
- [Pseudo-Bag Mixup Augmentation for Multiple Instance Learning-Based Whole Slide Image Classification](https://mlsanity.com/paper/2306.16180/) (2023)
- [PLUTO: Pathology-Universal Transformer](https://mlsanity.com/paper/2405.07905/) (2024)
- [Benchmarking Pathology Foundation Models: Adaptation Strategies and Scenarios](https://mlsanity.com/paper/2410.16038/) (2024)
- [A Survey on Computational Pathology Foundation Models: Datasets, Adaptation Strategies, and Evaluation Tasks](https://mlsanity.com/paper/2501.15724/) (2025)

## Abstract (arXiv)

Computational pathology can lead to saving human lives, but models are annotation hungry and pathology images are notoriously expensive to annotate. Self-supervised learning has shown to be an effective method for utilizing unlabeled data, and its application to pathology could greatly benefit its downstream tasks. Yet, there are no principled studies that compare SSL methods and discuss how to adapt them for pathology. To address this need, we execute the largest-scale study of SSL pre-training on pathology image data, to date. Our study is conducted using 4 representative SSL methods on diverse downstream tasks. We establish that large-scale domain-aligned pre-training in pathology consistently out-performs ImageNet pre-training in standard SSL settings such as linear and fine-tuning evaluations, as well as in low-label regimes. Moreover, we propose a set of domain-specific techniques that we experimentally show leads to a performance boost. Lastly, for the first time, we apply SSL to the challenging task of nuclei instance segmentation and show large and consistent performance improvements under diverse settings.